This vignette is intended to document basic functionality of the ecositer package. This package is in development and should not be expected to perform in a robust manner across different datasets. At this point, the functionality here is a demonstration of workflows for dealing with NRCS ecological site data. I hope that future development of this package and standardization of NASIS population will make it more applicable.
Library
library(ecositer)
library(soilDB)
library(dplyr)
library(DT)
library(indicspecies)
library(stringr)
library(listviewer)
library(plotly)
library(knitr)
library(kableExtra)Begin by querying NASIS so that you have a selected set containing vegetation data. In this vignette, we will query for vegetation data in Sequoia and Kings Canyon National Parks, soil survey area CA792. Detailed instructions for making this query can be found here.
Now that we have data in our selected set, we will introduce the
first ecositer function. vegStaticNASIS() takes a
snapshot of your NASIS selected set and saves it in a local SQLite
database. It is referred to as “static” because it does not change. This
means that regardless of what is in your selected set in the future, you
can refer to this static NASIS database using a local file path on your
harddrive. Rather than switching between different queries and clearing
your selected set in NASIS, you will likely find it useful to save a few
specific selected sets locally on your computer. The functionality of
creating static NASIS selected sets is borrowed from soilDB.
vegStaticNASIS() is a special case designed specifically
for vegetation data.
The only argument in this function is output_path the
local file path where you want to save your static NASIS database.
ecositer::vegStaticNASIS(output_path = "C:/Users/Nathan.Roe/Documents/SEKI/CA792_veg.sqlite")Let’s start off by looking at how many pedons and vegplots we have for each ecosite
numb_plots <- number_plots_by_site(static_location = "C:/Users/Nathan.Roe/Documents/SEKI/CA792_veg.sqlite")
knitr::kable(numb_plots)| ecositeid | ecosite_simple | pedons | vegplots | numb_statephases | statephases |
|---|---|---|---|---|---|
| NA | NA | 163 | 1078 | 1 | NA |
| F022AD102CA | D102 | 78 | 35 | 4 | D102.1.1, D102.1.1P, D102.1.2F, D102.1.3F |
| F022AH102CA | H102 | 61 | 26 | 4 | H102.1.4F, H102.1.1, H102.1.2F, H102.1.2A |
| F022AD104CA | D104 | 50 | 33 | 2 | D104.1.1, D104.1.4F |
| F022AH106CA | H106 | 39 | 25 | 2 | H106.1.1, H106.1.3F |
| F022AH101CA | H101 | 38 | 19 | 4 | H101.1.2F, H101.1.1, H101.1.3F, H101.1.4F |
| F022AB100CA | B100 | 33 | 32 | 3 | B100.1.1, B100.1.2F, B100.1.3F |
| F022AB114CA | B114 | 33 | 27 | 2 | B114.1.1, B114.1.3A |
| R022AB006CA | B006 | 33 | 31 | 3 | B006.1.1, B006.1.3E, B006.1.3A |
| R022AD002CA | D002 | 33 | 13 | 3 | D002.1.1, D002.1.3F, D002.1.2F |
| F022AB113CA | B113 | 31 | 24 | 4 | B113.1.1, B113.1.2F, B113.1.3A, B113.1.1P |
| F022AB111CA | B111 | 30 | 33 | 4 | B111.1.4A, B111.1.1, B111.1.2F, B111.1.3F |
| R022AD007CA | D007 | 28 | 17 | 3 | D007.1.3F, D007.1.2F, D007.1.1 |
| R022AX008CA | X008 | 28 | 23 | 1 | X008.1.1 |
| R022AX011CA | X011 | 27 | 9 | 5 | X011.1.2G, X011.1.1, X011.1.3G, X011.1.3E, X011.1.4G |
| R022AA102CA | A102 | 26 | 19 | 2 | A102.1.1, A102.1.1M |
| F022AH104CA | H104 | 25 | 22 | 2 | H104.1.3F, H104.1.1 |
| R022AB001CA | B001 | 25 | 17 | 1 | B001.1.1 |
| R022AD003CA | D003 | 25 | 19 | 4 | D003.1.1, D003.1.3A, D003.1.3F, D003.1.2F |
| F022AD103CA | D103 | 24 | 25 | 4 | D103.1.4F, D103.1.1, D103.1.2F, D103.1.3F |
| R022AH000CA | H000 | 24 | 16 | 4 | H000.1.2A, H000.1.1, H000.1.3F, H000.1.1P |
| R022AA106CA | A106 | 23 | 17 | 1 | A106.1.1 |
| F022AK100CA | K100 | 22 | 13 | 3 | K100.1.1, K100.1.4G, K100.1.2F |
| F018XC201CA | C201 | 21 | 13 | 3 | C201.1.3G, C201.1.2F, C201.1.1 |
| R022AK002CA | K002 | 21 | 16 | 5 | K002.1.3F, K002.1.1P, K002.1.1, K002.1.2F, K002.1.4F |
| R022AD001CA | D001 | 20 | 21 | 4 | D001.1.4A, D001.1.3A, D001.1.1, D001.1.2A |
| F018XC203CA | C203 | 19 | 8 | 3 | C203.1.1, C203.1.3G, C203.1.4G |
| R018XC107CA | C107 | 19 | 4 | 2 | C107.1.1, C107.1 |
| F022AD100CA | D100 | 17 | 17 | 4 | D100.1.2F, D100.1.1, D100.1.3F, D100.1.4F |
| R022AA010CA | A010 | 16 | 7 | 2 | A010.1.2A, A010.1.1 |
| R022AD009CA | D009 | 16 | 10 | 2 | D009.1.1, D009.1.1P |
| F022AX017CA | X017 | 15 | 10 | 3 | X017.1.1, X017.1.2U, X017.1.3U |
| R022AH001CA | H001 | 15 | 9 | 3 | H001.1.1, H001.1.2F, H001.1.3F |
| F022AX005CA | X005 | 14 | 12 | 3 | X005.1.1, X005.1.2F, X005.1.3A |
| R022AB010CA | B010 | 13 | 8 | 3 | B010.1.1, B010.1.4A, B010.1.2A |
| R022AX000CA | X000 | 13 | 19 | 4 | X000.1.3G, X000.1.4G, X000.1.1, X000.1.2G |
| F022AB108CA | B108 | 12 | 7 | 2 | B108.1.2F, B108.1.1 |
| R022AA107CA | A107 | 12 | 5 | 1 | A107.1.1 |
| R022AX006CA | X006 | 12 | 16 | 3 | X006.1.1, X006.1.1P, X006.1.1D |
| R022AX009CA | X009 | 12 | 8 | 2 | X009.1.3G, X009.1.1 |
| F022AD101CA | D101 | 11 | 7 | 3 | D101.1.1, D101.1.4F, D101.1.3F |
| F022AX013CA | X013 | 11 | 9 | 2 | X013.1.1, X013.1.3A |
| R022AD010CA | D010 | 11 | 1 | 1 | D010.1.2A |
| F022AH203CA | H203 | 10 | 9 | 3 | H203.1.1, H203.1.2F, H203.1.3F |
| R022AX010CA | X010 | 10 | 9 | 2 | X010.1.1P, X010.1.1 |
| F022AK101CA | K101 | 9 | 8 | 2 | K101.1.2F, K101.1.1 |
| R022AK001CA | K001 | 9 | 6 | 3 | K001.1.2F, K001.1.3F, K001.1.1 |
| R022AX007CA | X007 | 9 | 16 | 4 | X007.1.1, X007.1.3G, X007.1.1D, X007.1.4E |
| F018XC110CA | C110 | 8 | NA | NA | NA |
| F022AD105CA | D105 | 8 | 10 | 5 | D105.1.4F, D105.1.3F, D105.1.1, D105.1.1P, D105.1.2F |
| F022AK104CA | K104 | 8 | 6 | 4 | K104.1.1, K104.1.4G, K104.1.4B, K104.1.3F |
| F022AX014CA | X014 | 8 | 4 | 1 | X014.1.1 |
| R022AA101CA | A101 | 8 | 8 | 1 | A101.1.1 |
| R022AA104CA | A104 | 7 | NA | NA | NA |
| R022AB009CA | B009 | 7 | 5 | 2 | B009.1.1, B009.1.4A |
| F022AX003CA | X003 | 6 | 8 | 1 | X003.1.1 |
| R022AB004CA | B004 | 6 | 4 | 3 | B004.1.2F, B004.1.1, B004.1.3A |
| R022AX002CA | X002 | 6 | 7 | 3 | X002.1.1, X002.1.3E, X002.1.2A |
| R018XX101CA | X101 | 5 | NA | NA | NA |
| R022AX001CA | X001 | 5 | 9 | 3 | X001.1.1P, X001.1.1, X001.1.1D |
| F018XC109CA | C109 | 4 | 4 | 1 | C109.1.1 |
| F022AH201CA | H201 | 4 | 5 | 3 | H201.1.1, H201.1.2F, H201.1.3F |
| F022AH202CA | H202 | 4 | 5 | 2 | H202.1.3F, H202.1.2F |
| R022AB002CA | B002 | 3 | 2 | 1 | B002.1.1 |
| R022AB012CA | B012 | 3 | 2 | 1 | B012.1.1 |
| R022AX004CA | X004 | 2 | 6 | 1 | X004.1.1 |
| R018XX100CA | X100 | 1 | NA | NA | NA |
| R022AD004CA | D004 | 1 | 4 | 1 | D004.1.1 |
| R022AD005CA | D005 | 1 | NA | NA | NA |
| NA | X020 | NA | 11 | 3 | X020.1.1, X020.1.2G, X020.1.4A |
| NA | X016 | NA | 6 | 3 | X016.1.1M, X016.1.2F, X016.1.1 |
| NA | X199 | NA | 6 | 1 | X199.1.1 |
| NA | 1804 | NA | 3 | 2 | 1804.1.1, 1804.1.3F |
| NA | X999 | NA | 2 | 1 | X999.1.1 |
| NA | B007 | NA | 1 | 1 | B007.1.1P |
| NA | B008 | NA | 1 | 1 | B008.1.1 |
Now we can format our vegetation data into a more useful format
CA792_veg_formatted <- formatted_veg_df(static_location = "C:/Users/Nathan.Roe/Documents/SEKI/CA792_veg.sqlite")Here is a look at a portion of the data we have assembled.
DT::datatable(CA792_veg_formatted |> dplyr::select(-primarydatacollector, - plantnatvernm, -akfieldecositeid,
-vegplotid, -vegplotiid, -plantsym))Now that the data is formatted we can begin to analyze it.
CA792_veg_summary <- ecositer::veg_summary(veg_df = CA792_veg_formatted)The result of veg_summary() is a list. This list
provides a vegetation summary for every ecosite and state/phase in your
dataset, as well as raw dataset by ecosite and state/phase.
listviewer::jsonedit(CA792_veg_summary, width = 750)Now let’s look at a vegetation summary, including elements like importance, Indicator Species Analysis, and more.
CA792_veg_summary$R022AB006CA$Cover_data |> knitr::kable() |> kable_styling("striped",
full_width = TRUE) |> kableExtra::scroll_box(width = "750px", height = "500px")| constancy | avg_abund | twenty_percentile | eighty_percentile | median_abund | max_abund | min_abund | sum_abund | numb_plots_found | numb_plots_not_found | perc_obs_pres_abs | perc_obs_in_ecosite | perc_abund_in_ecosite | importance | ISA_p.value | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Juncus parryi | 83.870968 | 2.9774194 | 0.1 | 6.0 | 2.00 | 12.0 | 0 | 92.3 | 26 | 5 | 0 | 0.1125541 | 0.1283906 | 0.0144509 | NA |
| Pinus albicaulis | 70.967742 | 14.5419355 | 0.0 | 25.0 | 7.00 | 85.0 | 0 | 450.8 | 22 | 9 | 0 | 0.1788618 | 0.3384384 | 0.0605337 | NA |
| Carex rossii | 64.516129 | 0.5870968 | 0.0 | 1.0 | 0.75 | 3.0 | 0 | 18.2 | 20 | 11 | 0 | 0.1156069 | 0.0652096 | 0.0075387 | NA |
| Carex filifolia | 64.516129 | 10.3258065 | 0.0 | 22.0 | 13.00 | 50.0 | 0 | 320.1 | 20 | 11 | 0 | 0.1257862 | 0.1414682 | 0.0177947 | NA |
| Elymus elymoides | 58.064516 | 0.6451613 | 0.0 | 1.0 | 0.50 | 5.0 | 0 | 20.0 | 18 | 13 | 0 | 0.0983607 | 0.0888099 | 0.0087354 | NA |
| Poa secunda | 51.612903 | 0.4451613 | 0.0 | 1.0 | 0.75 | 2.0 | 0 | 13.8 | 16 | 15 | 0 | 0.1797753 | 0.1188630 | 0.0213686 | NA |
| Pinus contorta var. murrayana | 41.935484 | 1.6322581 | 0.0 | 2.5 | 2.50 | 19.0 | 0 | 50.6 | 13 | 18 | 0 | 0.0445205 | 0.0108731 | 0.0004841 | NA |
| Selaginella watsonii | 38.709677 | 0.7032258 | 0.0 | 2.0 | 2.00 | 4.0 | 0 | 21.8 | 12 | 19 | 0 | 0.1008403 | 0.0753283 | 0.0075961 | NA |
| Penstemon newberryi | 35.483871 | 1.1000000 | 0.0 | 2.0 | 2.00 | 12.0 | 0 | 34.1 | 11 | 20 | 0 | 0.1057692 | 0.2099754 | 0.0222089 | NA |
| Cistanthe umbellata var. umbellata | 32.258065 | 0.1516129 | 0.0 | 0.5 | 0.50 | 1.0 | 0 | 4.7 | 10 | 21 | 0 | 0.2127660 | 0.2701149 | 0.0574713 | 0.4 |
| Eriogonum ovalifolium | 22.580645 | 0.0774194 | 0.0 | 0.1 | 0.10 | 1.0 | 0 | 2.4 | 7 | 24 | 0 | 0.1944444 | 0.0933852 | 0.0181582 | NA |
| Trisetum spicatum | 22.580645 | 0.1838710 | 0.0 | 0.1 | 0.50 | 2.0 | 0 | 5.7 | 7 | 24 | 0 | 0.0744681 | 0.0553398 | 0.0041210 | NA |
| Eriogonum nudum | 22.580645 | 0.1322581 | 0.0 | 0.1 | 0.50 | 1.0 | 0 | 4.1 | 7 | 24 | 0 | 0.0777778 | 0.0686767 | 0.0053415 | NA |
| Eriogonum rosense | 22.580645 | 0.2580645 | 0.0 | 0.5 | 1.00 | 2.0 | 0 | 8.0 | 7 | 24 | 0 | 0.1555556 | 0.1199400 | 0.0186573 | NA |
| Achnatherum occidentale | 22.580645 | 0.2000000 | 0.0 | 0.1 | 0.50 | 3.0 | 0 | 6.2 | 7 | 24 | 0 | 0.0598291 | 0.0185462 | 0.0011096 | NA |
| Antennaria rosea | 19.354839 | 0.2967742 | 0.0 | 0.0 | 0.50 | 7.0 | 0 | 9.2 | 6 | 25 | 0 | 0.0714286 | 0.0676471 | 0.0048319 | NA |
| Antennaria | 19.354839 | 0.0870968 | 0.0 | 0.0 | 0.50 | 1.0 | 0 | 2.7 | 6 | 25 | 0 | 0.0740741 | 0.0147300 | 0.0010911 | NA |
| Penstemon | 19.354839 | 0.1967742 | 0.0 | 0.0 | 0.75 | 2.0 | 0 | 6.1 | 6 | 25 | 0 | 0.0937500 | 0.0729665 | 0.0068406 | NA |
| Arabis | 19.354839 | 0.0967742 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 3.0 | 6 | 25 | 0 | 0.0571429 | 0.0785340 | 0.0044877 | NA |
| Linanthus pungens | 19.354839 | 0.0580645 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 1.8 | 6 | 25 | 0 | 0.1428571 | 0.0687023 | 0.0098146 | NA |
| Penstemon rydbergii | 19.354839 | 0.2258065 | 0.0 | 0.0 | 1.00 | 2.0 | 0 | 7.0 | 6 | 25 | 0 | 0.1071429 | 0.0612423 | 0.0065617 | NA |
| Carex | 16.129032 | 0.0838710 | 0.0 | 0.0 | 0.50 | 1.0 | 0 | 2.6 | 5 | 26 | 0 | 0.0176678 | 0.0014559 | 0.0000257 | NA |
| Potentilla drummondii | 16.129032 | 0.0677419 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 2.1 | 5 | 26 | 0 | 0.1351351 | 0.0419162 | 0.0056643 | NA |
| Poa | 16.129032 | 0.1161290 | 0.0 | 0.0 | 0.50 | 2.0 | 0 | 3.6 | 5 | 26 | 0 | 0.0438596 | 0.0196399 | 0.0008614 | NA |
| Phyllodoce breweri | 12.903226 | 0.1935484 | 0.0 | 0.0 | 1.50 | 2.0 | 0 | 6.0 | 4 | 27 | 0 | 0.0384615 | 0.0066196 | 0.0002546 | NA |
| Eriogonum incanum | 12.903226 | 0.1612903 | 0.0 | 0.0 | 1.00 | 2.0 | 0 | 5.0 | 4 | 27 | 0 | 0.1333333 | 0.2732240 | 0.0364299 | NA |
| Solidago multiradiata | 12.903226 | 0.0387097 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 1.2 | 4 | 27 | 0 | 0.0579710 | 0.0076923 | 0.0004459 | NA |
| Ivesia | 12.903226 | 0.0967742 | 0.0 | 0.0 | 0.75 | 1.0 | 0 | 3.0 | 4 | 27 | 0 | 0.1481481 | 0.0471698 | 0.0069881 | NA |
| Achnatherum | 12.903226 | 0.0645161 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 2.0 | 4 | 27 | 0 | 0.0430108 | 0.0139958 | 0.0006020 | NA |
| Arabis platysperma | 9.677419 | 0.0387097 | 0.0 | 0.0 | 0.10 | 1.0 | 0 | 1.2 | 3 | 28 | 0 | 0.0857143 | 0.0909091 | 0.0077922 | NA |
| Penstemon heterodoxus | 9.677419 | 0.1000000 | 0.0 | 0.0 | 1.00 | 2.0 | 0 | 3.1 | 3 | 28 | 0 | 0.0857143 | 0.0780856 | 0.0066931 | NA |
| Poa stebbinsii | 9.677419 | 0.0387097 | 0.0 | 0.0 | 0.10 | 1.0 | 0 | 1.2 | 3 | 28 | 0 | 0.4285714 | 0.1621622 | 0.0694981 | NA |
| Ribes montigenum | 9.677419 | 0.0387097 | 0.0 | 0.0 | 0.10 | 1.0 | 0 | 1.2 | 3 | 28 | 0 | 0.0285714 | 0.0055607 | 0.0001589 | NA |
| Monardella odoratissima | 9.677419 | 0.0645161 | 0.0 | 0.0 | 0.50 | 1.0 | 0 | 2.0 | 3 | 28 | 0 | 0.0428571 | 0.0208986 | 0.0008957 | NA |
| Achillea millefolium | 9.677419 | 0.0645161 | 0.0 | 0.0 | 0.50 | 1.0 | 0 | 2.0 | 3 | 28 | 0 | 0.0329670 | 0.0253485 | 0.0008357 | NA |
| Holodiscus discolor | 9.677419 | 0.0225806 | 0.0 | 0.0 | 0.10 | 0.5 | 0 | 0.7 | 3 | 28 | 0 | 0.0447761 | 0.0027058 | 0.0001212 | NA |
| Pinus | 9.677419 | 0.4548387 | 0.0 | 0.0 | 5.10 | 8.5 | 0 | 14.1 | 3 | 28 | 0 | 0.2142857 | 0.0891841 | 0.0191109 | NA |
| Eriogonum | 9.677419 | 0.1774194 | 0.0 | 0.0 | 2.00 | 3.0 | 0 | 5.5 | 3 | 28 | 0 | 0.0769231 | 0.0418569 | 0.0032198 | NA |
| Rumex | 9.677419 | 0.0483871 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 1.5 | 3 | 28 | 0 | 0.1034483 | 0.1209677 | 0.0125139 | NA |
| Poa cusickii | 9.677419 | 0.0838710 | 0.0 | 0.0 | 0.50 | 2.0 | 0 | 2.6 | 3 | 28 | 0 | 0.0612245 | 0.0295791 | 0.0018110 | NA |
| Koeleria macrantha | 9.677419 | 0.1322581 | 0.0 | 0.0 | 2.00 | 2.0 | 0 | 4.1 | 3 | 28 | 0 | 0.0731707 | 0.0424870 | 0.0031088 | NA |
| Pinus balfouriana | 9.677419 | 0.3290323 | 0.0 | 0.0 | 5.00 | 5.1 | 0 | 10.2 | 3 | 28 | 0 | 0.0394737 | 0.0147955 | 0.0005840 | NA |
| Aster | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0270270 | 0.0034325 | 0.0000928 | NA |
| Gentianopsis simplex | 6.451613 | 0.0064516 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.2 | 2 | 29 | 0 | 0.2500000 | 0.0112360 | 0.0028090 | NA |
| Penstemon davidsonii | 6.451613 | 0.0064516 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.2 | 2 | 29 | 0 | 0.1052632 | 0.0117647 | 0.0012384 | NA |
| Raillardella scaposa | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.2222222 | 0.1224490 | 0.0272109 | NA |
| Salix orestera | 6.451613 | 0.1967742 | 0.0 | 0.0 | 3.05 | 6.0 | 0 | 6.1 | 2 | 29 | 0 | 0.0298507 | 0.0077147 | 0.0002303 | NA |
| Cryptogramma acrostichoides | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0555556 | 0.0491803 | 0.0027322 | NA |
| Sibbaldia procumbens | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0454545 | 0.0107720 | 0.0004896 | NA |
| Poa wheeleri | 6.451613 | 0.1935484 | 0.0 | 0.0 | 3.00 | 5.0 | 0 | 6.0 | 2 | 29 | 0 | 0.0338983 | 0.0256082 | 0.0008681 | NA |
| Heuchera rubescens | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0909091 | 0.0137931 | 0.0012539 | NA |
| Senecio | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0357143 | 0.0043259 | 0.0001545 | NA |
| Silene | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0909091 | 0.0487805 | 0.0044346 | NA |
| Silene lemmonii | 6.451613 | 0.0322581 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 1.0 | 2 | 29 | 0 | 0.3333333 | 0.7142857 | 0.2380952 | NA |
| Vaccinium cespitosum | 6.451613 | 0.2096774 | 0.0 | 0.0 | 3.25 | 6.0 | 0 | 6.5 | 2 | 29 | 0 | 0.0238095 | 0.0078465 | 0.0001868 | NA |
| Agrostis | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0588235 | 0.0026810 | 0.0001577 | NA |
| Muhlenbergia richardsonis | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0800000 | 0.0346821 | 0.0027746 | NA |
| Agrostis idahoensis | 6.451613 | 0.0322581 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 1.0 | 2 | 29 | 0 | 0.0416667 | 0.0027093 | 0.0001129 | NA |
| Antennaria corymbosa | 6.451613 | 0.0645161 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 2.0 | 2 | 29 | 0 | 0.0666667 | 0.0584795 | 0.0038986 | NA |
| Castilleja | 6.451613 | 0.0193548 | 0.0 | 0.0 | 0.30 | 0.5 | 0 | 0.6 | 2 | 29 | 0 | 0.0350877 | 0.0155844 | 0.0005468 | NA |
| Erigeron | 6.451613 | 0.0322581 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 1.0 | 2 | 29 | 0 | 0.0555556 | 0.0227790 | 0.0012655 | NA |
| Arenaria kingii | 6.451613 | 0.0677419 | 0.0 | 0.0 | 1.05 | 2.0 | 0 | 2.1 | 2 | 29 | 0 | 0.2857143 | 0.4468085 | 0.1276596 | NA |
| Potentilla | 6.451613 | 0.0354839 | 0.0 | 0.0 | 0.55 | 1.0 | 0 | 1.1 | 2 | 29 | 0 | 0.0289855 | 0.0133011 | 0.0003855 | NA |
| Symphoricarpos rotundifolius | 6.451613 | 0.0354839 | 0.0 | 0.0 | 0.55 | 1.0 | 0 | 1.1 | 2 | 29 | 0 | 0.0370370 | 0.0069975 | 0.0002592 | NA |
| Danthonia unispicata | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 0.1666667 | 0.0153846 | 0.0025641 | NA |
| Luzula subcongesta | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 0.0666667 | 0.0042553 | 0.0002837 | NA |
| Danthonia | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.1000000 | 0.0578035 | 0.0057803 | NA |
| Achnatherum latiglume | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.1666667 | 0.2325581 | 0.0387597 | NA |
| Castilleja applegatei | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0232558 | 0.0165563 | 0.0003850 | NA |
| Ribes | 3.225807 | 0.0967742 | 0.0 | 0.0 | 3.00 | 3.0 | 0 | 3.0 | 1 | 30 | 0 | 0.0119048 | 0.0157978 | 0.0001881 | NA |
| Salix | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0147059 | 0.0007350 | 0.0000108 | NA |
| Achnatherum pinetorum | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.5000000 | 0.8333333 | 0.4166667 | NA |
| Ericameria | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.3333333 | 0.7142857 | 0.2380952 | NA |
| Poa fendleriana | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.1250000 | 0.0709220 | 0.0088652 | NA |
| Rhodiola integrifolia ssp. integrifolia | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0666667 | 0.0833333 | 0.0055556 | NA |
| Ribes cereum | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0144928 | 0.0038521 | 0.0000558 | NA |
| Rumex acetosella | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.1111111 | 0.1515152 | 0.0168350 | NA |
| Luzula | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0476190 | 0.0222222 | 0.0010582 | NA |
| Ivesia santolinoides | 3.225807 | 0.3225806 | 0.0 | 0.0 | 10.00 | 10.0 | 0 | 10.0 | 1 | 30 | 0 | 0.1000000 | 0.3378378 | 0.0337838 | NA |
| Lupinus albicaulis | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0769231 | 0.0274725 | 0.0021133 | NA |
| Festuca | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0666667 | 0.1136364 | 0.0075758 | NA |
| Microseris | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.1428571 | 0.1136364 | 0.0162338 | NA |
| Phlox diffusa | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0769231 | 0.0373134 | 0.0028703 | NA |
| Sphenosciadium capitellatum | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0277778 | 0.0081169 | 0.0002255 | NA |
| Antennaria pulchella | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.1111111 | 0.0319489 | 0.0035499 | NA |
| Muhlenbergia filiformis | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0357143 | 0.0044683 | 0.0001596 | NA |
| Oreostemma peirsonii | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0909091 | 0.0284091 | 0.0025826 | NA |
| Potentilla glandulosa | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0400000 | 0.0322581 | 0.0012903 | NA |
| Sedum | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0500000 | 0.0122249 | 0.0006112 | NA |
| Elymus trachycaulus ssp. trachycaulus | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0322581 | 0.0051867 | 0.0001673 | NA |
| Juncus orthophyllus | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0909091 | 0.0116550 | 0.0010595 | NA |
| Oreostemma alpigenum var. andersonii | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0109890 | 0.0006044 | 0.0000066 | NA |
| Pedicularis attollens | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0476190 | 0.0357143 | 0.0017007 | NA |
| Eragrostis intermedia | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.2500000 | 0.0892857 | 0.0223214 | NA |
| Hieracium horridum | 3.225807 | 0.0161290 | 0.0 | 0.0 | 0.50 | 0.5 | 0 | 0.5 | 1 | 30 | 0 | 0.0166667 | 0.0251256 | 0.0004188 | NA |
| Calochortus | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.0714286 | 0.3846154 | 0.0274725 | NA |
| Raillardella argentea | 3.225807 | 0.0645161 | 0.0 | 0.0 | 2.00 | 2.0 | 0 | 2.0 | 1 | 30 | 0 | 0.3333333 | 0.9090909 | 0.3030303 | 0.9 |
| Selaginella | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.3333333 | 0.8333333 | 0.2777778 | 0.9 |
| Cirsium | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 0.0434783 | 0.0031949 | 0.0001389 | NA |
| Oreonana | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 1.0000000 | 1.0000000 | 1.0000000 | 0.9 |
| Ericameria discoidea | 3.225807 | 0.0322581 | 0.0 | 0.0 | 1.00 | 1.0 | 0 | 1.0 | 1 | 30 | 0 | 0.1428571 | 0.5000000 | 0.0714286 | NA |
| Artemisia tridentata ssp. vaseyana | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 0.0196078 | 0.0003382 | 0.0000066 | NA |
| Lonicera | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 0.0384615 | 0.0052910 | 0.0002035 | NA |
| Phlox | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 0.0294118 | 0.0020284 | 0.0000597 | NA |
| Lupinus lepidus | 3.225807 | 0.0032258 | 0.0 | 0.0 | 0.10 | 0.1 | 0 | 0.1 | 1 | 30 | 0 | 0.0250000 | 0.0009116 | 0.0000228 | NA |
| Calamagrostis breweri | 3.225807 | 0.0645161 | 0.0 | 0.0 | 2.00 | 2.0 | 0 | 2.0 | 1 | 30 | 0 | 0.0136986 | 0.0018260 | 0.0000250 | NA |
One useful tool for looking at ecological data is Non-Metric Multidimensional Scaling.
my_nmds <- ecositer::nmds_ecosite(veg_summary = CA792_veg_summary, ecosite = c("F022AK100CA", "F022AK101CA"), pres_abs = TRUE, nmds_dim = 2, reduce_species = NA)
#> Run 0 stress 0.1920348
#> Run 1 stress 0.1943657
#> Run 2 stress 0.1943972
#> Run 3 stress 0.2243439
#> Run 4 stress 0.1920353
#> ... Procrustes: rmse 0.0003189586 max resid 0.001551779
#> ... Similar to previous best
#> Run 5 stress 0.2252217
#> Run 6 stress 0.2182233
#> Run 7 stress 0.194454
#> Run 8 stress 0.2016835
#> Run 9 stress 0.1946112
#> Run 10 stress 0.195011
#> Run 11 stress 0.2183573
#> Run 12 stress 0.1994242
#> Run 13 stress 0.1948882
#> Run 14 stress 0.1922434
#> ... Procrustes: rmse 0.01143298 max resid 0.03565544
#> Run 15 stress 0.1920421
#> ... Procrustes: rmse 0.007718833 max resid 0.03140165
#> Run 16 stress 0.2039612
#> Run 17 stress 0.1998307
#> Run 18 stress 0.2279321
#> Run 19 stress 0.1994438
#> Run 20 stress 0.2219273
#> Run 21 stress 0.2018171
#> Run 22 stress 0.1923712
#> ... Procrustes: rmse 0.02039892 max resid 0.09053014
#> Run 23 stress 0.2275599
#> Run 24 stress 0.2242465
#> Run 25 stress 0.194366
#> Run 26 stress 0.194591
#> Run 27 stress 0.2206002
#> Run 28 stress 0.1943978
#> Run 29 stress 0.2161539
#> Run 30 stress 0.1952732
#> Run 31 stress 0.1944228
#> Run 32 stress 0.1920359
#> ... Procrustes: rmse 0.0005662958 max resid 0.002767675
#> ... Similar to previous best
#> Run 33 stress 0.2224874
#> Run 34 stress 0.194675
#> Run 35 stress 0.1944978
#> Run 36 stress 0.2284606
#> Run 37 stress 0.2068999
#> Run 38 stress 0.1920438
#> ... Procrustes: rmse 0.007926858 max resid 0.03128936
#> Run 39 stress 0.2069103
#> Run 40 stress 0.1963972
#> Run 41 stress 0.2047695
#> Run 42 stress 0.2364156
#> Run 43 stress 0.2155448
#> Run 44 stress 0.204869
#> Run 45 stress 0.1944059
#> Run 46 stress 0.220569
#> Run 47 stress 0.2252724
#> Run 48 stress 0.1920611
#> ... Procrustes: rmse 0.008930358 max resid 0.03074702
#> Run 49 stress 0.1944069
#> Run 50 stress 0.1920417
#> ... Procrustes: rmse 0.002178437 max resid 0.01072892
#> *** Best solution repeated 2 timesVisualize NMDS
nmds_plot(static_location = "C:/Users/Nathan.Roe/Documents/SEKI/CA792_veg.sqlite",
nmds = my_nmds,
veg_summary = CA792_veg_summary)